Functional Enrichment Analysis | Tool: gprofileR.
net_dir = "/pastel/projects/speakeasy_dlpfc/SpeakEasy_singlenuclei/2nd_pass/snakemake-sn/results/"
macro_type = params$cell_type #macro_structure. It can be cell_type, metabolites, region of the brain.
message(paste0("Cluster: ", macro_type))## Cluster: ast
We removed the clusters with < 30 nodes for downstream analysis.
modules_file = read.table(paste0(net_dir, macro_type, "/geneBycluster.txt"), header = T)
modules_file = modules_file[, c("gene_name", "cluster_lv3")]
modules_file$module_clusters = paste0("m", modules_file$cluster_lv3)
modules_file$cluster_lv3 = NULL
colnames(modules_file) = c("symbol", "module_clusters") #only the sn was with gene_name instead of symbol
modules_size = as.data.frame(table(modules_file$module_clusters))
colnames(modules_size) = c("module", "n_nodes")
createDT(modules_size)sessionInfo()R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Stream 8
Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] DT_0.20 plotly_4.10.0 knitr_1.37 gprofiler2_0.2.1 ggeasy_0.1.3 readxl_1.3.1 kableExtra_1.3.4 R.matlab_3.6.2 forcats_0.5.1 stringr_1.4.0
[11] dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 tidyverse_1.3.1 limma_3.50.1 ggfortify_0.4.14 ggplot2_3.3.5
loaded via a namespace (and not attached): [1] bitops_1.0-7 fs_1.5.2 lubridate_1.8.0 webshot_0.5.2 RColorBrewer_1.1-2 httr_1.4.2 tools_4.1.2 backports_1.4.1 bslib_0.3.1
[10] utf8_1.2.2 R6_2.5.1 vipor_0.4.5 DBI_1.1.2 lazyeval_0.2.2 colorspace_2.0-3 withr_2.4.3 tidyselect_1.1.2 gridExtra_2.3
[19] compiler_4.1.2 cli_3.2.0 rvest_1.0.2 xml2_1.3.3 sass_0.4.0 scales_1.1.1 systemfonts_1.0.4 digest_0.6.29 rmarkdown_2.11
[28] svglite_2.1.0 R.utils_2.11.0 pkgconfig_2.0.3 htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.1 rstudioapi_0.13
[37] shiny_1.7.1 jquerylib_0.1.4 generics_0.1.2 jsonlite_1.7.3 crosstalk_1.2.0 R.oo_1.24.0 RCurl_1.98-1.6 magrittr_2.0.2 Rcpp_1.0.8
[46] ggbeeswarm_0.6.0 munsell_0.5.0 fansi_1.0.2 lifecycle_1.0.1 R.methodsS3_1.8.1 stringi_1.7.6 yaml_2.3.5 grid_4.1.2 promises_1.2.0.1
[55] crayon_1.5.0 haven_2.4.3 hms_1.1.1 pillar_1.7.0 reprex_2.0.1 glue_1.6.1 evaluate_0.15 data.table_1.14.2 modelr_0.1.8
[64] httpuv_1.6.5 vctrs_0.3.8 tzdb_0.2.0 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 xfun_0.29 mime_0.12 xtable_1.8-4
[73] broom_0.7.12 later_1.3.0 viridisLite_0.4.0 pheatmap_1.0.12 beeswarm_0.4.0 ellipsis_0.3.2